arXiv subjects

Nicolas Behr

Publications and source records attributed to Nicolas Behr.

At least 19 recordsLinked to original sources

arXiv2022

Tracelet Hopf Algebras and Decomposition Spaces (Extended Abstract)

Tracelets are the intrinsic carriers of causal information in categorical rewriting systems. In this work, we assemble tracelets into a symmetric monoidal decomposition space, inducing a cocommutative Hopf algebra of tracelets. This Hopf algebra captures important combinatorial and algebraic aspects of rewriting theory, and is motivated by applications of its representation theory to stochastic rewriting systems such as chemical reaction networks.

cs.LO↗

arXiv2022

Fundamentals of Compositional Rewriting Theory

A foundational theory of compositional categorical rewriting theory is presented, based on a collection of fibration-like properties that collectively induce and intrinsically structure the large collection of lemmata used in the proofs of theorems such as concurrency and associativity. The resulting highly generic proofs of these theorems are given. It is noteworthy that the proof of the concurrency theorem takes only a few lines and, while that of associativity remains somewhat longer, it would be unreadably long if written directly in terms of the basic lemmata. In essence, our framework improves the readability and ease of comprehension of these proofs by exposing latent modularity. A curated list of known instances of our framework is used to conclude the paper with a detailed discussion of the conditions under which the Double Pushout and Sesqui-Pushout semantics of graph transformation are compositional.

cs.LO↗

arXiv2021

Stochastic Graph Transformation For Social Network Modeling

Adaptive networks model social, physical, technical, or biological systems as attributed graphs evolving at the level of both their topology and data. They are naturally described by graph transformation, but the majority of authors take an approach inspired by the physical sciences, combining an informal description of the operations with programmed simulations, and systems of ODEs as the only abstract mathematical description. We show that we can capture a range of social network models, the so-called voter models, as stochastic attributed graph transformation systems, demonstrate the benefits of this representation and establish its relation to the non-standard probabilistic view adopted in the literature. We use the theory and tools of graph transformation to analyze and simulate the models and propose a new variant of a standard stochastic simulation algorithm to recreate the results observed.

cs.DM↗

arXiv2021

Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics (Long version)

The Kappa biochemistry and the MØD organic chemistry frameworks are amongst the most intensely developed applications of rewriting-based methods in the life sciences to date. A typical feature of these types of rewriting theories is the necessity to implement certain structural constraints on the objects to be rewritten (a protein is empirically found to have a certain signature of sites, a carbon atom can form at most four bonds, ...). In this paper, we contribute a number of original developments that permit to implement a universal theory of continuous-time Markov chains (CTMCs) for stochastic rewriting systems. Our core mathematical concepts are a novel rule algebra construction for the relevant setting of rewriting rules with conditions, both in Double- and in Sesqui-Pushout semantics, augmented by a suitable stochastic mechanics formalism extension that permits to derive dynamical evolution equations for pattern-counting statistics. A second main contribution of our paper is a novel framework of restricted rewriting theories, which comprises a rule-algebra calculus under the restriction to so-called constraint-preserving completions of application conditions (for rules considered to act only upon objects of the underlying category satisfying a globally fixed set of structural constraints). This novel framework in turn renders a faithful encoding of bio- and organo-chemical rewriting in the sense of Kappa and MØD possible, which allows us to derive a rewriting-based formulation of reaction systems including a full-fledged CTMC semantics as instances of our universal CTMC framework. While offering an interesting new perspective and conceptual simplification of this semantics in the setting of Kappa, both the formal encoding and the CTMC semantics of organo-chemical reaction systems as motivated by the MØD framework are the first such results of their kind.

cs.LO↗

arXiv2021

Concurrency Theorems for Non-linear Rewriting Theories

Sesqui-pushout (SqPO) rewriting along non-linear rules and for monic matches is well-known to permit the modeling of fusing and cloning of vertices and edges, yet to date, no construction of a suitable concurrency theorem was available. The lack of such a theorem, in turn, rendered compositional reasoning for such rewriting systems largely infeasible. We develop in this paper a suitable concurrency theorem for non-linear SqPO-rewriting in categories that are quasi-topoi (subsuming the example of adhesive categories) and with matches required to be regular monomorphisms of the given category. Our construction reveals an interesting "backpropagation effect" in computing rule compositions. We derive in addition a concurrency theorem for non-linear double pushout (DPO) rewriting in rm-adhesive categories. Our results open non-linear SqPO and DPO semantics to the rich static analysis techniques available from concurrency, rule algebra and tracelet theory.

cs.LO↗

arXiv2021

On Stochastic Rewriting and Combinatorics via Rule-Algebraic Methods

Building upon the rule-algebraic stochastic mechanics framework, we present new results on the relationship of stochastic rewriting systems described in terms of continuous-time Markov chains, their embedded discrete-time Markov chains and certain types of generating function expressions in combinatorics. We introduce a number of generating function techniques that permit a novel form of static analysis for rewriting systems based upon marginalizing distributions over the states of the rewriting systems via pattern-counting observables.

cs.LO↗

arXiv2021

Fusion of interfaces in Landau-Ginzburg models: a functorial approach

We investigate the fusion of B-type interfaces in two-dimensional supersymmetric Landau-Ginzburg models. In particular, we propose to describe the fusion of an interface in terms of a fusion functor that acts on the category of modules of the underlying polynomial rings of chiral superfields. This uplift of a functor on the category of matrix factorisations simplifies the actual computation of interface fusion. Besides a brief discussion of minimal models, we illustrate the power of this approach in the SU(3)/U(2) Kazama-Suzuki model where we find fusion functors for a set of elementary topological defects from which all rational B-type topological defects can be generated.

hep-th↗

arXiv2020

Efficient Computation of Graph Overlaps for Rule Composition: Theory and Z3 Prototyping

Graph transformation theory relies upon the composition of rules to express the effects of sequences of rules. In practice, graphs are often subject to constraints, ruling out many candidates for composed rules. Focusing on the case of sesqui-pushout (SqPO) semantics, we develop a number of alternative strategies for computing compositions, each theoretically and with an implementation via the Python API of the Z3 theorem prover. The strategies comprise a straightforward generate-and-test strategy based on forbidden graph patterns, a variant with a more implicit logical encoding of the negative constraints, and a modular strategy, where the patterns are decomposed as forbidden relation patterns. For a toy model of polymer formation in organic chemistry, we compare the performance of the three strategies in terms of execution times and memory consumption.

cs.LO↗

arXiv2020

Tracelets and Tracelet Analysis Of Compositional Rewriting Systems

Taking advantage of a recently discovered associativity property of rule compositions, we extend the classical concurrency theory for rewriting systems over adhesive categories. We introduce the notion of tracelets, which are defined as minimal derivation traces that universally encode sequential compositions of rewriting rules. Tracelets are compositional, capture the causality of equivalence classes of traditional derivation traces, and intrinsically suggest a clean mathematical framework for the definition of various notions of abstractions of traces. We illustrate these features by introducing a first prototype for a framework of tracelet analysis, which as a key application permits to formulate a first-of-its-kind algorithm for the static generation of minimal derivation traces with prescribed terminal events.

cs.LO↗

arXiv2020

Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics

The Kappa biochemistry and the MØD organo-chemistry frameworks are amongst the most intensely developed applications of rewriting theoretical methods in the life sciences to date. A typical feature of these types of rewriting theories is the necessity to implement certain structural constraints on the objects to be rewritten (a protein is empirically found to have a certain signature of sites, a carbon atom can form at most four bonds, ...). In this paper, we contribute to the theoretical foundations of these types of rewriting theory a number of conceptual and technical developments that permit to implement a universal theory of continuous-time Markov chains (CTMCs) for stochastic rewriting systems. Our core mathematical concepts are a novel rule algebra construction for the relevant setting of rewriting rules with conditions, both in Double- and in Sesqui-Pushout semantics, augmented by a suitable stochastic mechanics formalism extension that permits to derive dynamical evolution equations for pattern-counting statistics.

cs.LO↗

arXiv2019

Sesqui-Pushout Rewriting: Concurrency, Associativity and Rule Algebra Framework

Sesqui-pushout (SqPO) rewriting is a variant of transformations of graph-like and other types of structures that fit into the framework of adhesive categories where deletion in unknown context may be implemented. We provide the first account of a concurrency theorem for this important type of rewriting, and we demonstrate the additional mathematical property of a form of associativity for these theories. Associativity may then be exploited to construct so-called rule algebras (of SqPO type), based upon which in particular a universal framework of continuous-time Markov chains for stochastic SqPO rewriting systems may be realized.

cs.LO↗

arXiv2019

Dual Numbers and Operational Umbral Methods

Dual numbers and their higher order version are important tools for numerical computations, and in particular for finite difference calculus. Based upon the relevant algebraic rules and matrix realizations of dual numbers, we will present a novel point of view, embedding dual numbers within a formalism reminiscent of operational umbral calculus.

math.GM↗

arXiv2019

Compositionality of Rewriting Rules with Conditions

We extend the notion of compositional associative rewriting as recently studied in the rule algebra framework literature to the setting of rewriting rules with conditions. Our methodology is category-theoretical in nature, where the definition of rule composition operations encodes the non-deterministic sequential concurrent application of rules in Double-Pushout (DPO) and Sesqui-Pushout (SqPO) rewriting with application conditions based upon $\mathcal{M}$-adhesive categories. We uncover an intricate interplay between the category-theoretical concepts of conditions on rules and morphisms, the compositionality and compatibility of certain shift and transport constructions for conditions, and thirdly the property of associativity of the composition of rules.

cs.LO↗

arXiv2019

Combinatorial Conversion and Moment Bisimulation for Stochastic Rewriting Systems

We develop a novel method to analyze the dynamics of stochastic rewriting systems evolving over finitary adhesive, extensive categories. Our formalism is based on the so-called rule algebra framework and exhibits an intimate relationship between the combinatorics of the rewriting rules (as encoded in the rule algebra) and the dynamics which these rules generate on observables (as encoded in the stochastic mechanics formalism). We introduce the concept of combinatorial conversion, whereby under certain technical conditions the evolution equation for (the exponential generating function of) the statistical moments of observables can be expressed as the action of certain differential operators on formal power series. This permits us to formulate the novel concept of moment-bisimulation, whereby two dynamical systems are compared in terms of their evolution of sets of observables that are in bijection. In particular, we exhibit non-trivial examples of graphical rewriting systems that are moment-bisimilar to certain discrete rewriting systems (such as branching processes or the larger class of stochastic chemical reaction systems). Our results point towards applications of a vast number of existing well-established exact and approximate analysis techniques developed for chemical reaction systems to the far richer class of general stochastic rewriting systems.

cs.LO↗

arXiv2019

Operator Ordering and Solution of Pseudo-Evolutionary Equations

The solution of pseudo initial value differential equations, either ordinary or partial (including those of fractional nature), requires the development of adequate analytical methods, complementing those well established in the ordinary differential equation setting. A combination of techniques, involving procedures of umbral and of operational nature, has been demonstrated to be a very promising tool in order to approach within a unifying context non-canonical evolution problems. This article covers the extension of this approach to the solution of pseudo-evolutionary equations. We will comment on the explicit formulation of the necessary techniques, which are based on certain time- and operator ordering tools. We will in particular demonstrate how Volterra-Neumann expansions, Feynman-Dyson series and other popular tools can be profitably extended to obtain solutions of fractional differential equations. We apply the method to a number of examples, in which fractional calculus and a certain umbral image calculus play a role of central importance.

math-ph↗

arXiv2019

Operational Methods in the Study of Sobolev-Jacobi Polynomials

Inspired by ideas from umbral calculus and based on the two types of integrals occurring in the defining equations for the gamma and the reciprocal gamma functions, respectively, we develop a multi-variate version of umbral calculus and of the so-called umbral image technique. Besides providing a class of new formulae for generalized hypergeometric functions and an implementation of series manipulations for computing lacunary generating functions, our main application of these techniques is the study of Sobolev-Jacobi polynomials. Motivated by applications to theoretical chemistry, we moreover present a deep link between generalized normal-ordering techniques introduced by Gurappa and Panigrahi, two-variable Hermite polynomials and our integral-based series transforms. Notably, we thus calculate all K-tuple L-shifted lacunary exponential generating functions for a certain family of SJ polynomials explicitly.

math-ph↗

arXiv2018

Rule Algebras for Adhesive Categories

We demonstrate that the most well-known approach to rewriting graphical structures, the Double-Pushout (DPO) approach, possesses a notion of sequential compositions of rules along an overlap that is associative in a natural sense. Notably, our results hold in the general setting of $\mathcal{M}$-adhesive categories. This observation complements the classical Concurrency Theorem of DPO rewriting. We then proceed to define rule algebras in both settings, where the most general categories permissible are the finitary (or finitary restrictions of) $\mathcal{M}$-adhesive categories with $\mathcal{M}$-effective unions. If in addition a given such category possess an $\mathcal{M}$-initial object, the resulting rule algebra is unital (in addition to being associative). We demonstrate that in this setting a canonical representation of the rule algebras is obtainable, which opens the possibility of applying the concept to define and compute the evolution of statistical moments of observables in stochastic DPO rewriting systems.

cs.LO↗

arXiv2018

Explicit formulae for all higher order exponential lacunary generating functions of Hermite polynomials

For a sequence $P=(p_n(x))_{n=0}^{\infty}$ of polynomials $p_n(x)$, we study the $K$-tuple and $L$-shifted exponential lacunary generating functions $\mathcal{G}_{K,L}(λ;x):=\sum_{n=0}^{\infty}\frac{λ^n}{n!} p_{n\cdot K+L}(x)$, for $K=1,2\dotsc$ and $L=0,1,2\dotsc$. We establish an algorithm for efficiently computing $\mathcal{G}_{K,L}(λ;x)$ for generic polynomial sequences $P$. This procedure is exemplified by application to the study of Hermite polynomials, whereby we obtain closed-form expressions for $\mathcal{G}_{K,L}(λ;x)$ for arbitrary $K$ and $L$, in the form of infinite series involving generalized hypergeometric functions. The basis of our method is provided by certain resummation techniques, supplemented by operational formulae. Our approach also reproduces all the results previously known in the literature.

math-ph↗